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  Dynamics of the B-A transition of DNA double helices

Jose, D., & Porschke, D. (2004). Dynamics of the B-A transition of DNA double helices. Nucleic Acids Research, 32(7), 2251-2258. Retrieved from http://nar.oxfordjournals.org/cgi/content/full/32/7/2251.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0012-EEB4-0 Version Permalink: http://hdl.handle.net/21.11116/0000-0002-032E-8
Genre: Journal Article

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Jose, D.1, Author              
Porschke, D.1, Author              
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1Research Group of Biomolecular Dynamics, MPI for biophysical chemistry, Max Planck Society, ou_578610              

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 Abstract: Although the transition from the B-DNA double helix to the A-form is essential for biological function, as shown by the existence of the A-form in many protein–DNA complexes, the dynamics of this transition has not been resolved yet. According to molecular dynamics simulations the transition is expected in the time range of a few nanoseconds. The B–A transition induced by mixing of DNA samples with ethanol in stopped flow experiments is complete within the deadtime, showing that the reaction is faster than ~0.2 ms. The reaction was resolved by an electric field jump technique with induction of the transition by a dipole stretching force driving the A- to the B-form. Poly[d(A-T)] was established as a favourable model system, because of a particularly high cooperativity of the transition and because of a spectral signature allowing separation of potential side reactions. The time constants observed in the case of poly[d(A-T)] with ~1600 bp are in the range around 10 µs. An additional process with time constants of ~100 µs is probably due to nucleation. The same time constants (within experimental accuracy ±10%) were observed for a poly[d(A-T)] sample with ~70 bp. Under low salt conditions commonly used for studies of the B–A transition, the time constants are almost independent of the ionic strength. The experimental data show that a significant activation barrier exists in the B–A transition and that the helical states are clearly separated from each other, in contrast to predictions by molecular dynamics simulations.

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Language(s): eng - English
 Dates: 2004-07-282004
 Publication Status: Published in print
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 Rev. Method: Peer
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Title: Nucleic Acids Research
Source Genre: Journal
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Pages: - Volume / Issue: 32 (7) Sequence Number: - Start / End Page: 2251 - 2258 Identifier: -